Woolsey has Ronon come in for a meeting about the fact he hasn't made any mission reports despite Woolsey's new policy on everyone making a mission report. Ronon either doesn't remember, doesn't care, or both. Woolsey gives him a voice recorder and tells him to make his reports on that if he can't provide a written report. Meanwhile, Sheppard and Rodney are racing RC cars in the corridors when they almost knock over Teyla. She's trying to get a restless Torren to sleep for the night. She leaves them to it and goes back to her quarters, and gets back as the power goes out.
Rodney and Sheppard can't raise anyone on the radio and head back to base, while Teyla finds herself trapped in her quarters. The door opens but the repair team she expects isn't there: two other men stun her and take her away. Meanwhile, Sheppard and Rodney meet up with the rest of the Atlantis staff and realize that the control tower has been sealed off and everyone inside of it is trapped. The stairwell doors are sealed and they assume that someone has infiltrated the base. Their theory is confirmed when Rodney and Zelenka discover that all critical systems have been locked out from the control room. They tape into the security cameras in the tower, which are a non-critical system, and see a Jumper parked in front of the Stargate. Accessing the camera in Woolsey's office, they see... Michael. He has Teyla and Torren with her and is explaining to her that he captured a team and took their access code. He and his team of hybrid soldiers signaled for access, Woolsey let them in, and the Jumper projected a force field with a stun device, knocking out the tower staff.
Michael plans to activate Atlantis' self-destruct to punish the expedition for "creating him." However, he tells Teyla that Torren will be safe. While Sheppard prepares an assault once they get the stairwell doors open, Ronon wakes up among the tower staff, in a locked room.
One of Michael's soldiers warns him that they're having trouble activating the self-destruct and suggests they leave now that they have what they came for, rather than risk capture. Michael tells them to continue with the plan. Meanwhile, the two assault teams blow open the stairwell doors and move upward, but Rodney senses an energy field ahead. He's too late to warn Lorne's team, and the major walks into an energy field designed to stun anyone coming into contact with it. Zelenka and Rodney determine that Michael is using the generator on his stolen Jumper to power the stun field and power the override of the tower systems.
While Rodney and Zelenka try to figure out a way to override the generator, Banks wakes up in the tower and goes to work on the sealed doors. Michael says that Teyla can come along with him and promises not to harm her or Torren, but she doesn't believe him.
With no other options, Sheppard tells Rodney to prepare a Jumper so he can fly it up to the tower and use drones to destroy Michael's Jumper. However, Rodney tells him that they only have two Jumpers on base outside of the tower are in the flooded section, and he hasn't gotten around to repairing either one yet. Sheppard takes Rodney to fix them. Meanwhile, Banks gets the door open and she fights one of the hybrid soldiers long enough for Ronon to stun it. Woolsey and the rest of the tower staff start to wake up and Ronon sneaks into the control room to determine how many soldiers Michael brought with him. He reports back and they go to the armory, but before they can get there overhear Michael's men reporting that they've decoded the self-destruct and are prepared to activate it. Ronon tells Woolsey to go back and goes to the control room to stop Michael.
In Woolsey's office, Teyla steals a communication device and tries to contact Sheppard without success. Ronon arrives and tells her to warn, then attacks Michael and his people. She runs off and finds Woolsey, and the two of them run away from one of the hybrids. Michael and Ronon fight and Michael eventually overpowers Ronon and throws him off a balcony to the floor below, knocking him out.
Zelenka reports what's happened to Sheppard, while Rodney figures out how to put together a working Jumper using parts from both damaged vehicles. Meanwhile, Teyla and Woolsey discover the teleporters are shut down and flee down the stairs. Woolsey, in the lead, unwittingly walks into the stun field and is knocked out. Teyla knocks the pursuing hybrid into the stun field and then hides in an access panel.
Rodney gets the Jumper working but discovers he can't get the drones to function. Sheppard decides they have no other choice but for him to fly their Jumper into Michael's. Meanwhile, a frustrated Michael activates the self-destruct after his soldiers report they're unable to find Teyla. He calls to her over the intercom and promises to shut down the self-destruct if she surrenders.
As Sheppard prepares to fly to the control tower, Zelenka regains partial control and informs Sheppard of their status, including the fact they can now drop the Gate shield. They come up with a new plan: Sheppard will lead an assault while Rodney flies the Jumper up to the tower and activates the DHD. The wormhole will destroy Michael's Jumper and the generator inside, giving them access.
Teyla finally offers to surrender but demands that Michael shut down the self-destruct first. He refuses, telling her he has a sample of Torren's DNA and doesn't need her. Michael and the remaining soldiers prepare to leave but he stops to kill the unconscious Ronon first. As he prepares to deliver the killing blow, the Gate opens and the wormhole disintegrates the back half of his Jumper. Sheppard and his soldiers charge in and open fire, and a battle ensues. Sheppard wounds Michael, who flees toward the Jumper bay. Teyla emerges from hiding, gives Torren to Banks, and runs after Michael and Sheppard.
With the bay doors sealed, the wounded Michael flees to an outer ledge. Sheppard comes after him and the two struggle. Michael knocks Sheppard down to a lower platform and jumps down after him. Despite his injury, Michael gets the upper hand and prepares to throw Sheppard to his death. Teyla arrives and she and Sheppard knock Sheppard off the ledge. He hangs on to a support beam, but an angry Teyla kicks his hands free and he plummets dozens of stories to his death.
After mopping up, Ronon is taken to the infirmary and Woolsey congratulates him on his heroic actions. Ronon gives him the voice recorder with his mission report: it's very very short. Rodney and Sheppard are racing again and Teyla comes by, telling them that Torren was quiet the entire night during Michael's assault. As the guys go back to racing, Teyla figures that someone else will come after them some day, but Sheppard assures her that as long as she's there they have nothing to worry about.
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